Hi,
With the convenience that seqnamesStyles offers now, having to specify
the chromosome name notation manually would feel like a step back. In
terms of subsetting genomic ranges, I normally think of four major
groups of interest:
- Toplevel/standard: 1,..22,X,Y,MT
- Autosomes: 1,..,22
- A
The dropSeqlevels approach for the autosomes is acceptable in terms of
readability, but it means the code needs to know the seqname style (chrX
rather than just X).
On Fri, Dec 27, 2013 at 1:49 PM, Valerie Obenchain wrote:
> I think the idea was to avoid the proliferation of small, specialized
>
I think the idea was to avoid the proliferation of small, specialized
functions.
library(TxDb.Hsapiens.UCSC.hg19.knownGene)
gr <- transcripts(TxDb.Hsapiens.UCSC.hg19.knownGene)
## autosomes
std <- keepStandardChromosomes(gr, "Homo sapiens", "UCSC")
dropSeqlevels(std, c("chrX", "chrY"))
## allo
Hi Sonali,
Thank you for this much requested addition to the GenomicRanges API!
I would like to second Michael Lawrence's assertion that keepAutosomes() is
more straightforward and harder to misunderstand or misuse than a special case
of keep/dropSeqlevels. (If the author of a function has tr
Michael,
Since there is no universal seqnameStyle defined for various objects and
they do not internally store the seqnameStyle and species information,
we decided to ask the user for all 3 arguments. Marc is aware of these
issues and my code.
Regarding the dependency of GenomicRanges on Anno
I guess you mean dropSeqlevels, not keepSeqlevels? That should work. But
your function needs some tweaking, I think. The function should just take
the seqnameStyle from the object. There's no need to require the user to
specify it, and then check for consistency. I would like to be able to just
cal
Hi Michael,
We decided to come up with one function called keepStandardChromosomes()
which
is a wrapper for both the functions suggested by you (i.e.,
keepPrimaryChromosomes() and keepAutosomes() )
Here is an example:
library(AnnotationDbi)
library(GenomicRanges)
txdb <- loadDb(system.file("ext
Awesome -- how about keepAutosomes?
On Tue, Dec 24, 2013 at 1:11 PM, Arora, Sonali wrote:
> Hi everyone,
>
> We are pleased to announce that we have added a new function called
> keepStandardChromosomes() to GenomicRanges(1.15.18) - devel branch.
>
> This function allows a user to subset a g
Hi everyone,
We are pleased to announce that we have added a new function called
keepStandardChromosomes() to GenomicRanges(1.15.18) - devel branch.
This function allows a user to subset a given object (containing a
seqinfo class) to
retain only the primary chromosomes and the autosomes.
Plea
Awesome, thanks, Sonali. And welcome to the team.
Michael
On Mon, Dec 16, 2013 at 10:38 AM, Arora, Sonali wrote:
> Hi Michael,
>
> That is an extremely interesting question. We have a couple of ideas and
> are beginning to work on it.
> We hope to come up with something soon.
>
> Thanks,
> Son
Hi Michael,
That is an extremely interesting question. We have a couple of ideas and
are beginning to work on it.
We hope to come up with something soon.
Thanks,
Sonali.
On 12/16/2013 6:14 AM, Michael Lawrence wrote:
should be stored with the Seqinfo. It could be imputed
(along with the is
On Mon, Dec 16, 2013 at 5:00 AM, Julian Gehring wrote:
> Hi Michael,
>
> I would second your request. In a package I'll submitting soon, I have a
> work-around for this by defining a set of functions like 'hsAutosomes',
> 'hsAllosomes' etc. that return the respective set of human chromosome
> nam
Hi Michael,
I would second your request. In a package I'll submitting soon, I have
a work-around for this by defining a set of functions like
'hsAutosomes', 'hsAllosomes' etc. that return the respective set of
human chromosome names. Perhaps on could incorporate this in the
'seqinfo' class,
Is this being taken into consideration by anyone? Will it be worked on?
Thanks,
Michael
On Thu, Dec 12, 2013 at 1:36 PM, Michael Lawrence wrote:
> We've found that analysts often need to restrict seqlevels to certain
> pre-defined sets of chromsomes. Given the variability across organisms, it
We've found that analysts often need to restrict seqlevels to certain
pre-defined sets of chromsomes. Given the variability across organisms, it
would be nice to have an abstraction.
We often see this in code:
keepSeqlevels(seqinfo, as.character(1:22)
keepSeqlevels(seqinfo, c(1:22, "X", "Y"))
Pe
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